Medical tomography images like CT, MRI, PET, SPECT, fMRI, ett have been widely used for diagnosis and treatment of a patient and for clinical study in hospital. In many cases, tomography images are scanned in several different modalities or with time intervals for a single subject for extracting complementary information and comparing one another. 3D image registration is mapping two sets of images for comparison onto common 3D coordinate space, and may be categorized to marker -based matching and feature-based matching. 3D registration of brain images has an important role for visual and quantitative analysis in localization of treatment area of a brain, brain functional research, brain mapping research, and so on. In this article, marker-based and feature-based matching methods which are often used are introduced.